So, yeah, the 3-3-5 stack was sort of a spectacular failure. Not so much against the run, as Michigan did a decent job against Korey Sheets, but against the pass. Michigan allowed 266 yards—7.8 YPA—to a third string quarterback on a 2-6 team. That is epic failure.
Why did this happen? Well, IMO, the stack had a a major part in it. Here's a typical presnap alignment:
The thing to note is the one deep safety. This is Donovan Warren. With one deep safety the corners are basically on an island; they won't get much deep help from Warren on a sideline route. Fades and fly routes are going to be left up to the corner to defend.
Michigan, then, often sees itself play a cover-three susceptible to little hitches and out-cuts. Here's a closeup of Morgan Trent on one of many, many ten-yard outs that Purdue will find wide open all day:
We've just started the route. Greg Orton is going to run directly at Trent.
Trent is turning his hips inside and looking at the quarterback.
Here we see Orton reaching Trent, with Trent turned completely away from him, not even looking at him.
Orton begins his break with Trent facing 180 degrees the wrong way.
Orton now has two yards of separation and Trent is still facing the wrong way.
The perspective on this makes it difficult to tell, but this is wide open for ten yards.
Here's the video:
Michigan's corners have been coached to do this. Trent would do it all day, and Boubacar Cissoko did it on the long Orton completion down the sideline. This coverage style covers that extremely well and the only thing that made that a completion was a perfectly thrown ball, some bad luck on Cissoko's part not to knock it down, and a great catch by Orton.
However, every wide open hitch or out was because of it, too. It's completely impossible to flip your hips around 180 degrees that quickly, impossible to do anything but tackle after a first down. So Michigan provided this n00b quarterback with the easiest reads in the history of reads most of the day, and ended up paying for it.